Even though Atkins recommends mostly whole foods, the emphasis is still wrong in my opinion. He argues against carbohydrate and in favour of fat and not much else. You can't blame people for getting the main message and applying it beyond what's recommended in the book. Low-carb tortillas, pasta, shakes, are still low-carb, aren't they? Atkins even had his own line of frankenfoods.

I agree to a point. I think the main difference is that Atkins sees nothing wrong with grains, and PB does. Like I said before, I think PB takes what Atkins teaches and then does it one better, or several better, which I like!